Index

_

__call__() (pypesto.objective.AmiciObjective method) (pypesto.objective.ObjectiveBase method) (pypesto.predict.AmiciPredictor method) (pypesto.startpoint.CheckedStartpoints method) (pypesto.startpoint.NoStartpoints method) (pypesto.startpoint.StartpointMethod method) __init__() (pypesto.engine.Engine method) (pypesto.engine.MultiProcessEngine method) (pypesto.engine.MultiThreadEngine method) (pypesto.engine.SingleCoreEngine method) (pypesto.engine.Task method) (pypesto.ensemble.Ensemble method) (pypesto.ensemble.EnsemblePrediction method) (pypesto.history.CountHistoryBase method) (pypesto.history.CsvHistory method) (pypesto.history.CsvHistoryTemplateError method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.HistoryOptions method) (pypesto.history.HistoryTypeError method) (pypesto.history.MemoryHistory method) (pypesto.history.OptimizerHistory method) (pypesto.objective.AggregatedObjective method) (pypesto.objective.AmiciObjective method) (pypesto.objective.FD method) (pypesto.objective.FDDelta method) (pypesto.objective.julia.JuliaObjective method) (pypesto.objective.NegLogParameterPriors method) (pypesto.objective.Objective method) (pypesto.objective.ObjectiveBase method) (pypesto.optimize.CESSOptimizer method) (pypesto.optimize.CmaesOptimizer method) (pypesto.optimize.DlibOptimizer method) (pypesto.optimize.ESSOptimizer method) (pypesto.optimize.FidesOptimizer method) (pypesto.optimize.IpoptOptimizer method) (pypesto.optimize.NLoptOptimizer method) (pypesto.optimize.OptimizeOptions method) (pypesto.optimize.Optimizer method) (pypesto.optimize.PyswarmOptimizer method) (pypesto.optimize.PyswarmsOptimizer method) (pypesto.optimize.SacessOptimizer method) (pypesto.optimize.ScipyDifferentialEvolutionOptimizer method) (pypesto.optimize.ScipyOptimizer method) (pypesto.petab.PetabImporter method) (pypesto.petab.PetabImporterPysb method) (pypesto.predict.AmiciPredictor method) (pypesto.predict.PredictorTask method) (pypesto.problem.Problem method) (pypesto.profile.ProfileOptions method) (pypesto.result.McmcPtResult method) (pypesto.result.OptimizeResult method) (pypesto.result.OptimizerResult method) (pypesto.result.PredictionConditionResult method) (pypesto.result.PredictionResult method) (pypesto.result.ProfileResult method) (pypesto.result.ProfilerResult method) (pypesto.result.Result method) (pypesto.result.SampleResult method) (pypesto.sample.AdaptiveMetropolisSampler method) (pypesto.sample.DynestySampler method) (pypesto.sample.EmceeSampler method) (pypesto.sample.MetropolisSampler method) (pypesto.sample.ParallelTemperingSampler method) (pypesto.sample.Sampler method) (pypesto.select.Problem method) (pypesto.startpoint.CheckedStartpoints method) (pypesto.startpoint.FunctionStartpoints method) (pypesto.startpoint.LatinHypercubeStartpoints method) (pypesto.startpoint.UniformStartpoints method) (pypesto.store.OptimizationResultHDF5Reader method) (pypesto.store.OptimizationResultHDF5Writer method) (pypesto.store.ProblemHDF5Reader method) (pypesto.store.ProblemHDF5Writer method) (pypesto.store.ProfileResultHDF5Reader method) (pypesto.store.ProfileResultHDF5Writer method) (pypesto.store.SamplingResultHDF5Reader method) (pypesto.store.SamplingResultHDF5Writer method) (pypesto.visualize.ReferencePoint method)

A

AdaptiveMetropolisSampler (class in pypesto.sample) AdaptiveParallelTemperingSampler (class in pypesto.sample) adjust_betas() (pypesto.sample.AdaptiveParallelTemperingSampler method) (pypesto.sample.ParallelTemperingSampler method) AggregatedObjective (class in pypesto.objective) ALL_KEYS (pypesto.history.HistoryBase attribute) ALWAYS (pypesto.objective.FDDelta attribute) AmiciObjective (class in pypesto.objective) AmiciPredictor (class in pypesto.predict) append() (pypesto.result.OptimizeResult method) append_empty_profile_list() (pypesto.result.ProfileResult method) append_profile_point() (pypesto.result.ProfilerResult method) append_profiler_result() (pypesto.result.ProfileResult method)

apply_custom_timepoints() (pypesto.objective.AmiciObjective method) apply_steadystate_guess() (pypesto.objective.AmiciObjective method) approximate_parameter_profile() (in module pypesto.profile) as_dataframe() (pypesto.result.OptimizeResult method) as_list() (pypesto.result.OptimizeResult method) assert_instance() (pypesto.history.HistoryOptions static method) (pypesto.optimize.OptimizeOptions static method) assign_clustered_colors() (in module pypesto.visualize) assign_clusters() (in module pypesto.visualize) assign_colors() (in module pypesto.visualize) auto_color (pypesto.visualize.ReferencePoint attribute) auto_correlation() (in module pypesto.sample) autosave() (in module pypesto.store)

B

BACKWARD (pypesto.objective.FD attribute)

C

calculate_approximate_ci() (in module pypesto.profile) calculate_ci_mcmc_sample() (in module pypesto.sample) calculate_ci_mcmc_sample_prediction() (in module pypesto.sample) calibrated_models (pypesto.select.Problem attribute) call_unprocessed() (pypesto.objective.AggregatedObjective method) (pypesto.objective.AmiciObjective method) (pypesto.objective.FD method) (pypesto.objective.NegLogParameterPriors method) (pypesto.objective.Objective method) (pypesto.objective.ObjectiveBase method) CENTRAL (pypesto.objective.FD attribute) CESSOptimizer (class in pypesto.optimize) check_and_resample() (pypesto.startpoint.CheckedStartpoints method) check_grad() (pypesto.objective.ObjectiveBase method) check_grad_multi_eps() (pypesto.objective.ObjectiveBase method) check_gradients() (pypesto.petab.PetabImporter method) check_gradients_match_finite_differences() (pypesto.objective.AmiciObjective method) (pypesto.objective.ObjectiveBase method) check_identifiability() (pypesto.ensemble.Ensemble method) check_mode() (pypesto.objective.AggregatedObjective method) (pypesto.objective.AmiciObjective method) (pypesto.objective.NegLogParameterPriors method) (pypesto.objective.ObjectiveBase method) check_sensi_orders() (pypesto.objective.AggregatedObjective method) (pypesto.objective.AmiciObjective method) (pypesto.objective.NegLogParameterPriors method) (pypesto.objective.ObjectiveBase method)

CheckedStartpoints (class in pypesto.startpoint) chi2_quantile_to_ratio() (in module pypesto.profile) CmaesOptimizer (class in pypesto.optimize) color (pypesto.visualize.ReferencePoint attribute) compile_model() (pypesto.petab.PetabImporter method) (pypesto.petab.PetabImporterPysb method) compute_chi2() (pypesto.ensemble.EnsemblePrediction method) compute_summary() (pypesto.ensemble.Ensemble method) (pypesto.ensemble.EnsemblePrediction method) condense_to_arrays() (pypesto.ensemble.EnsemblePrediction method) CONSTANT (pypesto.objective.FDDelta attribute) CountHistory (class in pypesto.history) CountHistoryBase (class in pypesto.history) create_edatas() (pypesto.petab.PetabImporter method) create_history() (in module pypesto.history) create_instance() (pypesto.profile.ProfileOptions static method) create_method_caller() (pypesto.select.Problem method) create_model() (pypesto.petab.PetabImporter method) create_objective() (pypesto.petab.PetabImporter method) create_predictor() (pypesto.petab.PetabImporter method) create_prior() (pypesto.petab.PetabImporter method) create_problem() (pypesto.petab.PetabImporter method) create_references() (in module pypesto.visualize) create_solver() (pypesto.petab.PetabImporter method) create_startpoint_method() (pypesto.petab.PetabImporter method) CsvHistory (class in pypesto.history) CsvHistoryTemplateError

D

default_options() (pypesto.sample.AdaptiveMetropolisSampler class method) (pypesto.sample.AdaptiveParallelTemperingSampler class method) (pypesto.sample.MetropolisSampler class method) (pypesto.sample.ParallelTemperingSampler class method) (pypesto.sample.Sampler class method)

delete_nan_inf() (in module pypesto.visualize) dim (pypesto.problem.Problem property) display_source_ipython() (in module pypesto.objective.julia) DISTANCE (pypesto.objective.FDDelta attribute) DlibOptimizer (class in pypesto.optimize) DynestySampler (class in pypesto.sample)

E

effective_sample_size() (in module pypesto.sample) EmceeSampler (class in pypesto.sample) Engine (class in pypesto.engine) Ensemble (class in pypesto.ensemble) ensemble_crosstab_scatter_lowlevel() (in module pypesto.visualize) ensemble_identifiability() (in module pypesto.visualize) ensemble_scatter_lowlevel() (in module pypesto.visualize) EnsemblePrediction (class in pypesto.ensemble) ess_init_args (pypesto.optimize.CESSOptimizer attribute)

ESSOptimizer (class in pypesto.optimize) execute() (pypesto.engine.Engine method) (pypesto.engine.MultiProcessEngine method) (pypesto.engine.MultiThreadEngine method) (pypesto.engine.SingleCoreEngine method) (pypesto.engine.Task method) (pypesto.predict.PredictorTask method) exitflag (pypesto.history.Hdf5History property) (pypesto.result.OptimizerResult attribute) exitflag_path (pypesto.result.ProfilerResult attribute)

F

FD (class in pypesto.objective) FDDelta (class in pypesto.objective) FidesOptimizer (class in pypesto.optimize) fill_result_from_history() (in module pypesto.optimize) finalize() (pypesto.history.CsvHistory method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.OptimizerHistory method) fix_parameters() (pypesto.problem.Problem method) flip_profile() (pypesto.result.ProfilerResult method) FORWARD (pypesto.objective.FD attribute)

from_optimization_endpoints() (pypesto.ensemble.Ensemble static method) from_optimization_history() (pypesto.ensemble.Ensemble static method) from_sample() (pypesto.ensemble.Ensemble static method) from_yaml() (pypesto.petab.PetabImporter static method) full_index_to_free_index() (pypesto.problem.Problem method) FunctionStartpoints (class in pypesto.startpoint) fval (pypesto.result.OptimizerResult attribute) (pypesto.visualize.ReferencePoint attribute) fval0 (pypesto.result.OptimizerResult attribute) fval_path (pypesto.result.ProfilerResult attribute) fx_best (pypesto.optimize.CESSOptimizer attribute)

G

get() (pypesto.objective.FDDelta method) (pypesto.objective.julia.JuliaObjective method) get_chi2_trace() (pypesto.history.HistoryBase method) get_config() (pypesto.objective.AggregatedObjective method) (pypesto.objective.AmiciObjective method) (pypesto.objective.Objective method) (pypesto.objective.ObjectiveBase method) get_covariance_matrix_parameters() (in module pypesto.ensemble) get_covariance_matrix_predictions() (in module pypesto.ensemble) get_default_options() (pypesto.optimize.DlibOptimizer method) (pypesto.optimize.Optimizer method) (pypesto.optimize.ScipyOptimizer method) get_epsilon_ball_initial_state() (pypesto.sample.EmceeSampler method) get_for_key() (pypesto.result.OptimizeResult method) get_full_matrix() (pypesto.problem.Problem method) get_full_vector() (pypesto.problem.Problem method) get_fval() (pypesto.objective.ObjectiveBase method) get_fval_trace() (pypesto.history.CountHistory method) (pypesto.history.CsvHistory method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.MemoryHistory method) (pypesto.history.NoHistory method) get_grad() (pypesto.objective.ObjectiveBase method) get_grad_trace() (pypesto.history.CountHistory method) (pypesto.history.CsvHistory method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.MemoryHistory method) (pypesto.history.NoHistory method) get_hess() (pypesto.objective.ObjectiveBase method) get_hess_trace() (pypesto.history.CountHistory method) (pypesto.history.CsvHistory method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.MemoryHistory method) (pypesto.history.NoHistory method) get_last_sample() (pypesto.sample.InternalSampler method) (pypesto.sample.MetropolisSampler method) get_original_samples() (pypesto.sample.DynestySampler method) get_parameter_prior_dict() (in module pypesto.objective) get_pca_representation_parameters() (in module pypesto.ensemble) get_pca_representation_predictions() (in module pypesto.ensemble) get_percentile_label() (in module pypesto.ensemble) get_profiler_result() (pypesto.result.ProfileResult method)

get_reduced_matrix() (pypesto.problem.Problem method) get_reduced_vector() (pypesto.problem.Problem method) get_res() (pypesto.objective.ObjectiveBase method) get_res_trace() (pypesto.history.CountHistory method) (pypesto.history.CsvHistory method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.MemoryHistory method) (pypesto.history.NoHistory method) get_samples() (pypesto.sample.DynestySampler method) (pypesto.sample.EmceeSampler method) (pypesto.sample.MetropolisSampler method) (pypesto.sample.ParallelTemperingSampler method) (pypesto.sample.Sampler method) get_schi2_trace() (pypesto.history.HistoryBase method) get_spectral_decomposition_lowlevel() (in module pypesto.ensemble) get_spectral_decomposition_parameters() (in module pypesto.ensemble) get_spectral_decomposition_predictions() (in module pypesto.ensemble) get_sres() (pypesto.objective.ObjectiveBase method) get_sres_trace() (pypesto.history.CountHistory method) (pypesto.history.CsvHistory method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.MemoryHistory method) (pypesto.history.NoHistory method) get_time_trace() (pypesto.history.CountHistory method) (pypesto.history.CsvHistory method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.MemoryHistory method) (pypesto.history.NoHistory method) get_trimmed_indices() (pypesto.history.HistoryBase method) get_umap_representation_parameters() (in module pypesto.ensemble) get_umap_representation_predictions() (in module pypesto.ensemble) get_x_trace() (pypesto.history.CountHistory method) (pypesto.history.CsvHistory method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.MemoryHistory method) (pypesto.history.NoHistory method) geweke_test() (in module pypesto.sample) grad (pypesto.result.OptimizerResult attribute) grad_min (pypesto.history.OptimizerHistory attribute) gradient_neg_log_density() (pypesto.objective.NegLogParameterPriors method) gradnorm_path (pypesto.result.ProfilerResult attribute)

H

handle_select_kwargs() (pypesto.select.Problem method) has_fun (pypesto.objective.FD property) (pypesto.objective.Objective property) (pypesto.objective.ObjectiveBase property) has_grad (pypesto.objective.FD property) (pypesto.objective.Objective property) (pypesto.objective.ObjectiveBase property) has_hess (pypesto.objective.FD property) (pypesto.objective.Objective property) (pypesto.objective.ObjectiveBase property) has_hessp (pypesto.objective.Objective property) (pypesto.objective.ObjectiveBase property) has_res (pypesto.objective.FD property) (pypesto.objective.Objective property) (pypesto.objective.ObjectiveBase property)

has_sres (pypesto.objective.FD property) (pypesto.objective.Objective property) (pypesto.objective.ObjectiveBase property) Hdf5History (class in pypesto.history) hess (pypesto.result.OptimizerResult attribute) hess_min (pypesto.history.OptimizerHistory attribute) hessian_neg_log_density() (pypesto.objective.NegLogParameterPriors method) hessian_vp_neg_log_density() (pypesto.objective.NegLogParameterPriors method) history (pypesto.objective.ObjectiveBase attribute) (pypesto.result.OptimizerResult attribute) HistoryBase (class in pypesto.history) HistoryOptions (class in pypesto.history) HistoryTypeError

I

i_iter (pypesto.optimize.CESSOptimizer attribute) id (pypesto.predict.PredictorTask attribute) (pypesto.result.OptimizerResult attribute) implements_trace() (pypesto.history.HistoryBase method) initialize() (pypesto.objective.AggregatedObjective method) (pypesto.objective.AmiciObjective method) (pypesto.objective.ObjectiveBase method) (pypesto.sample.AdaptiveMetropolisSampler method) (pypesto.sample.DynestySampler method) (pypesto.sample.EmceeSampler method) (pypesto.sample.MetropolisSampler method) (pypesto.sample.ParallelTemperingSampler method) (pypesto.sample.Sampler method)

InternalSampler (class in pypesto.sample) IpoptOptimizer (class in pypesto.optimize) is_least_squares() (pypesto.optimize.CmaesOptimizer method) (pypesto.optimize.DlibOptimizer method) (pypesto.optimize.FidesOptimizer method) (pypesto.optimize.IpoptOptimizer method) (pypesto.optimize.NLoptOptimizer method) (pypesto.optimize.Optimizer method) (pypesto.optimize.PyswarmOptimizer method) (pypesto.optimize.PyswarmsOptimizer method) (pypesto.optimize.ScipyDifferentialEvolutionOptimizer method) (pypesto.optimize.ScipyOptimizer method)

J

JuliaObjective (class in pypesto.objective.julia)

L

latin_hypercube() (in module pypesto.startpoint) LatinHypercubeStartpoints (class in pypesto.startpoint) lb (pypesto.problem.Problem property) lb_init (pypesto.problem.Problem property) legend (pypesto.visualize.ReferencePoint attribute)

load() (pypesto.history.Hdf5History static method) load_objective_config() (in module pypesto.store) log() (in module pypesto.logging) log_level_active() (in module pypesto.logging) log_to_console() (in module pypesto.logging) log_to_file() (in module pypesto.logging)

M

make_internal() (pypesto.sample.InternalSampler method) (pypesto.sample.MetropolisSampler method) max_iter (pypesto.optimize.CESSOptimizer attribute) max_walltime_s (pypesto.optimize.CESSOptimizer attribute) McmcPtResult (class in pypesto.result) MemoryHistory (class in pypesto.history) message (pypesto.history.Hdf5History property) (pypesto.result.OptimizerResult attribute) (pypesto.result.ProfilerResult attribute) method_caller (pypesto.select.Problem attribute) METHODS (pypesto.objective.FD attribute) MetropolisSampler (class in pypesto.sample) MIN_KEYS (pypesto.history.OptimizerHistory attribute) minimize() (in module pypesto.optimize) (pypesto.optimize.CESSOptimizer method) (pypesto.optimize.CmaesOptimizer method) (pypesto.optimize.DlibOptimizer method) (pypesto.optimize.ESSOptimizer method) (pypesto.optimize.FidesOptimizer method) (pypesto.optimize.IpoptOptimizer method) (pypesto.optimize.NLoptOptimizer method) (pypesto.optimize.Optimizer method) (pypesto.optimize.PyswarmOptimizer method) (pypesto.optimize.PyswarmsOptimizer method) (pypesto.optimize.SacessOptimizer method) (pypesto.optimize.ScipyDifferentialEvolutionOptimizer method) (pypesto.optimize.ScipyOptimizer method)

mode (pypesto.predict.PredictorTask attribute) MODEL_BASE_DIR (pypesto.petab.PetabImporter attribute) model_postprocessor (pypesto.select.Problem attribute) model_to_pypesto_problem() (in module pypesto.select) module pypesto.engine pypesto.ensemble pypesto.history pypesto.logging pypesto.objective pypesto.objective.julia pypesto.optimize pypesto.petab pypesto.predict pypesto.problem pypesto.profile pypesto.result pypesto.sample pypesto.select pypesto.startpoint pypesto.store pypesto.visualize pypesto.visualize.model_fit MultiProcessEngine (class in pypesto.engine) multistart_select() (pypesto.select.Problem method) MultiThreadEngine (class in pypesto.engine)

N

n_fval (pypesto.history.CountHistoryBase property) (pypesto.history.Hdf5History property) (pypesto.history.HistoryBase property) (pypesto.history.NoHistory property) (pypesto.result.OptimizerResult attribute) (pypesto.result.ProfilerResult attribute) n_grad (pypesto.history.CountHistoryBase property) (pypesto.history.Hdf5History property) (pypesto.history.HistoryBase property) (pypesto.history.NoHistory property) (pypesto.result.OptimizerResult attribute) (pypesto.result.ProfilerResult attribute) n_hess (pypesto.history.CountHistoryBase property) (pypesto.history.Hdf5History property) (pypesto.history.HistoryBase property) (pypesto.history.NoHistory property) (pypesto.result.OptimizerResult attribute) (pypesto.result.ProfilerResult attribute)

n_res (pypesto.history.CountHistoryBase property) (pypesto.history.Hdf5History property) (pypesto.history.HistoryBase property) (pypesto.history.NoHistory property) (pypesto.result.OptimizerResult attribute) n_sres (pypesto.history.CountHistoryBase property) (pypesto.history.Hdf5History property) (pypesto.history.HistoryBase property) (pypesto.history.NoHistory property) (pypesto.result.OptimizerResult attribute) neg_log_density() (pypesto.objective.NegLogParameterPriors method) NegLogParameterPriors (class in pypesto.objective) NegLogPriors (class in pypesto.objective) newly_calibrated_models (pypesto.select.Problem attribute) NLoptOptimizer (class in pypesto.optimize) NoHistory (class in pypesto.history) normalize() (pypesto.problem.Problem method) NoStartpoints (class in pypesto.startpoint)

O

Objective (class in pypesto.objective) ObjectiveBase (class in pypesto.objective) optimization_result_from_history() (in module pypesto.optimize) optimization_run_properties_one_plot() (in module pypesto.visualize) optimization_run_properties_per_multistart() (in module pypesto.visualize) optimization_run_property_per_multistart() (in module pypesto.visualize) optimization_scatter() (in module pypesto.visualize) OptimizationResultHDF5Reader (class in pypesto.store) OptimizationResultHDF5Writer (class in pypesto.store) optimize_result (pypesto.result.Result attribute)

OptimizeOptions (class in pypesto.optimize) Optimizer (class in pypesto.optimize) optimizer (pypesto.result.OptimizerResult attribute) optimizer_convergence() (in module pypesto.visualize) optimizer_history() (in module pypesto.visualize) optimizer_history_lowlevel() (in module pypesto.visualize) OptimizeResult (class in pypesto.result) OptimizerHistory (class in pypesto.history) OptimizerResult (class in pypesto.result) output_to_tuple() (pypesto.objective.ObjectiveBase static method)

P

par_arr_to_dct() (pypesto.objective.AmiciObjective method) ParallelTemperingSampler (class in pypesto.sample) parameter_hist() (in module pypesto.visualize) parameter_profile() (in module pypesto.profile) parameters() (in module pypesto.visualize) parameters_lowlevel() (in module pypesto.visualize) petab_select_problem (pypesto.select.Problem attribute) PetabImporter (class in pypesto.petab) PetabImporterPysb (class in pypesto.petab) pre_post_processor (pypesto.objective.ObjectiveBase attribute) predict() (pypesto.ensemble.Ensemble method) prediction_to_petab_measurement_df() (pypesto.petab.PetabImporter method) prediction_to_petab_simulation_df() (pypesto.petab.PetabImporter method) PredictionConditionResult (class in pypesto.result) PredictionResult (class in pypesto.result) predictor (pypesto.predict.PredictorTask attribute) PredictorTask (class in pypesto.predict) print_parameter_summary() (pypesto.problem.Problem method) prior_transform() (pypesto.sample.DynestySampler method) Problem (class in pypesto.problem) (class in pypesto.select) problem (pypesto.result.Result attribute) ProblemHDF5Reader (class in pypesto.store) ProblemHDF5Writer (class in pypesto.store) process_offset_y() (in module pypesto.visualize) process_result_list() (in module pypesto.visualize) process_y_limits() (in module pypesto.visualize) profile_cis() (in module pypesto.visualize) profile_lowlevel() (in module pypesto.visualize) profile_result (pypesto.result.Result attribute) ProfileOptions (class in pypesto.profile) ProfileResult (class in pypesto.result) ProfileResultHDF5Reader (class in pypesto.store) ProfileResultHDF5Writer (class in pypesto.store) ProfilerResult (class in pypesto.result) profiles() (in module pypesto.visualize) profiles_lowlevel() (in module pypesto.visualize) projection_scatter_pca() (in module pypesto.visualize) projection_scatter_umap() (in module pypesto.visualize)

projection_scatter_umap_original() (in module pypesto.visualize) pypesto.engine module pypesto.ensemble module pypesto.history module pypesto.logging module pypesto.objective module pypesto.objective.julia module pypesto.optimize module pypesto.petab module pypesto.predict module pypesto.problem module pypesto.profile module pypesto.result module pypesto.sample module pypesto.select module pypesto.startpoint module pypesto.store module pypesto.visualize module pypesto.visualize.model_fit module PyswarmOptimizer (class in pypesto.optimize) PyswarmsOptimizer (class in pypesto.optimize)

R

ratio_path (pypesto.result.ProfilerResult attribute) rdatas_to_measurement_df() (pypesto.petab.PetabImporter method) rdatas_to_simulation_df() (pypesto.petab.PetabImporter method) read() (pypesto.store.OptimizationResultHDF5Reader method) (pypesto.store.ProblemHDF5Reader method) (pypesto.store.ProfileResultHDF5Reader method) (pypesto.store.SamplingResultHDF5Reader method) read_ensemble_prediction_from_h5() (in module pypesto.ensemble) read_from_csv() (in module pypesto.ensemble) read_from_df() (in module pypesto.ensemble) read_result() (in module pypesto.store)

read_result_from_file() (in module pypesto.optimize) read_results_from_file() (in module pypesto.optimize) recover_options() (pypesto.history.Hdf5History method) ReferencePoint (class in pypesto.visualize) res (pypesto.result.OptimizerResult attribute) res_min (pypesto.history.OptimizerHistory attribute) reset_steadystate_guesses() (pypesto.objective.AmiciObjective method) residual() (pypesto.objective.NegLogParameterPriors method) residual_jacobian() (pypesto.objective.NegLogParameterPriors method) restore_internal_sampler() (pypesto.sample.DynestySampler method) Result (class in pypesto.result) RESULT_KEYS (pypesto.history.HistoryBase attribute)

S

SacessOptimizer (class in pypesto.optimize) sample() (in module pypesto.sample) (pypesto.sample.DynestySampler method) (pypesto.sample.EmceeSampler method) (pypesto.sample.MetropolisSampler method) (pypesto.sample.ParallelTemperingSampler method) (pypesto.sample.Sampler method) (pypesto.startpoint.CheckedStartpoints method) (pypesto.startpoint.FunctionStartpoints method) (pypesto.startpoint.LatinHypercubeStartpoints method) sample_result (pypesto.result.Result attribute) Sampler (class in pypesto.sample) SampleResult (class in pypesto.result) sampling_1d_marginals() (in module pypesto.visualize) sampling_fval_traces() (in module pypesto.visualize) sampling_parameter_cis() (in module pypesto.visualize) sampling_parameter_traces() (in module pypesto.visualize) sampling_prediction_trajectories() (in module pypesto.visualize) sampling_scatter() (in module pypesto.visualize) SamplingResultHDF5Reader (class in pypesto.store) SamplingResultHDF5Writer (class in pypesto.store) save_internal_sampler() (pypesto.sample.DynestySampler method) ScipyDifferentialEvolutionOptimizer (class in pypesto.optimize) ScipyOptimizer (class in pypesto.optimize) select() (pypesto.select.Problem method) select_to_completion() (pypesto.select.Problem method) sensi_orders (pypesto.predict.PredictorTask attribute) set_custom_timepoints() (pypesto.objective.AmiciObjective method)

set_last_sample() (pypesto.sample.InternalSampler method) (pypesto.sample.MetropolisSampler method) set_profiler_result() (pypesto.result.ProfileResult method) set_state() (pypesto.select.Problem method) set_x_guesses() (pypesto.problem.Problem method) SingleCoreEngine (class in pypesto.engine) sort() (pypesto.result.OptimizeResult method) sres (pypesto.result.OptimizerResult attribute) sres_min (pypesto.history.OptimizerHistory attribute) start_time (pypesto.history.CountHistoryBase property) (pypesto.history.Hdf5History property) (pypesto.history.HistoryBase property) (pypesto.history.NoHistory property) StartpointMethod (class in pypesto.startpoint) starttime (pypesto.optimize.CESSOptimizer attribute) STEPS (pypesto.objective.FDDelta attribute) storage_filename (pypesto.store.OptimizationResultHDF5Reader attribute) (pypesto.store.OptimizationResultHDF5Writer attribute) (pypesto.store.ProblemHDF5Reader attribute) (pypesto.store.ProblemHDF5Writer attribute) (pypesto.store.ProfileResultHDF5Reader attribute) (pypesto.store.ProfileResultHDF5Writer attribute) (pypesto.store.SamplingResultHDF5Reader attribute) (pypesto.store.SamplingResultHDF5Writer attribute) store_steadystate_guess() (pypesto.objective.AmiciObjective method) summary() (pypesto.result.OptimizeResult method) (pypesto.result.OptimizerResult method) (pypesto.result.Result method) swap_samples() (pypesto.sample.ParallelTemperingSampler method)

T

Task (class in pypesto.engine) time (pypesto.result.OptimizerResult attribute) time_path (pypesto.result.ProfilerResult attribute) time_total (pypesto.result.ProfilerResult attribute)

time_trajectory_model() (in module pypesto.visualize.model_fit) to_startpoint_method() (in module pypesto.startpoint) trace_save_iter (pypesto.history.Hdf5History property) translate_options() (pypesto.sample.Sampler class method)

U

ub (pypesto.problem.Problem property) ub_init (pypesto.problem.Problem property) unfix_parameters() (pypesto.problem.Problem method) uniform() (in module pypesto.startpoint) UniformStartpoints (class in pypesto.startpoint) update() (pypesto.history.CountHistoryBase method) (pypesto.history.CsvHistory method) (pypesto.history.Hdf5History method) (pypesto.history.HistoryBase method) (pypesto.history.MemoryHistory method) (pypesto.history.NoHistory method) (pypesto.history.OptimizerHistory method) (pypesto.objective.FDDelta method)

UPDATE_CONDITIONS (pypesto.objective.FDDelta attribute) update_from_problem() (pypesto.objective.ObjectiveBase method) update_to_full() (pypesto.result.OptimizerResult method) update_with_newly_calibrated_models() (pypesto.select.Problem method)

V

validation_profile_significance() (in module pypesto.profile)

visualize_optimized_model_fit() (in module pypesto.visualize.model_fit)

W

waterfall() (in module pypesto.visualize) waterfall_lowlevel() (in module pypesto.visualize) write() (pypesto.store.OptimizationResultHDF5Writer method) (pypesto.store.ProblemHDF5Writer method) (pypesto.store.ProfileResultHDF5Writer method) (pypesto.store.SamplingResultHDF5Writer method)

write_array() (in module pypesto.store) write_ensemble_prediction_to_h5() (in module pypesto.ensemble) write_result() (in module pypesto.store) write_to_csv() (pypesto.result.PredictionResult method) write_to_h5() (pypesto.result.PredictionResult method)

X

x (pypesto.predict.PredictorTask attribute) (pypesto.result.OptimizerResult attribute) (pypesto.visualize.ReferencePoint attribute) x0 (pypesto.result.OptimizerResult attribute)

x_best (pypesto.optimize.CESSOptimizer attribute) x_free_indices (pypesto.problem.Problem property) x_guesses (pypesto.problem.Problem property) x_names (pypesto.objective.ObjectiveBase property) x_path (pypesto.result.ProfilerResult attribute)